AP Bio: Topic 2-6: Organic Chem

Organic Chemistry

The study of carbon based compounds that form the structural and functional foundation of all living things

Functional Groups

Specific groups of atoms within molecules that dictate the characteristic chemical reactions and physical composition of those compounds

• Hydroxyl, carbonyl, carboxyl, amines, and phosphate

• Functional groups dictate the chemical personality, shape, and behavior of organic molecules and living systems

ATP

Energy for living plants and animals

Macro-molecule

Large organic molecule built from smaller repeating subunits that’s essential for life

Organic Compounds

Carbon based molecules bonded with hydrogen, oxygen, nitrogen and other elements. They form the structural and functional bases of all living things

• Carbon’s atomic structure allows it to form stable, covalent bonds which makes it a versatile element

Hydrocarbons

Organic molecules that consist entirely of carbon and hydrogen atoms

Dehydration Reaction

Molecule loses water (H₂O) during transformation

• ie: H₃ PO₄ → HPO₃ + H20

Hydrolysis

Chemical reaction where water is used break down the bounds of a compound. Splits into smaller parts

• ie: AB +H20 → A-OH + B-H

Polymers

Large molecule made of many smaller, repeating, chemical units linked together

Monomers

Small simple molecules that can chemically bond with other similar molecules to form larger complex structures

Disaccharide

Type of sugar formed when 2 monossaccharides join together

Amino Acids

Organic molecules that combine to form proteins

• C, H, O, R, N

Cellulose

Gives plants their structure and rigidity. It’s a complex, fibrous, carbohydrate made up of thousands of glucose units

Polymer

A large chain formed when many monomers join together

Monosaccharide

Simplest carbohydrate form

• Remember 1:2:1

• consists of a single sugar unit

• CANT BE BROKEN DOWN INTO SMALLER PIECES

Glycogen

Branched polysaccharide that animals and fungi use to store excess glucose

Hydrophobic

“Afraid of water” Repels water or fails to mix with it

• think water and oil

Hydrphillic

“Water loving” Strongly attracted to water and mixes or dissolves easily in it

Polypeptides

Continuous chains of amino acids linked together by peptide bonds

Monomer

Small, basic building block that can chemically bond with similar/ identical molecules that form a larger → polymer

• there are 20 standard amino acid monomers for protein

Glycosidic Linkage

Covalent bond that joins a carbohydrate molecule to another group

• Forms from Dehydration Reaction

Starch

Complex carbohydrate and polysaccharide made of many glucose units joined together

• Macromolecule: Amylose and amylopectin

R-groups

Determines how amino acids interact and makes the final 3D shape

Polysaccharides

Large complex carbohydrate molecules made of many smaller sugar units linked together in long chains

• Energy storage and structure rigor for plants — +tissue structure in animals

Monomers of polysaccharides

Glucose, fructose, galactose, and moded sugars

How does saturation affect fatty acid structure and function?

Dictates biological function in cell membranes and energy storage

• Directly determines the shape, packing ability, and physical state of a fatty acid

Fat

Type of liquid made of glycerol and fatty acids that living things use to store energy

Fatty acid

Carboxylic acid with an aliphatic chain

• either saturated or unsaturated

Phospholipids

Fat molecule that can be found in the cell membrane of all living things.

• Forms main layer of the cell membrane and is the structural integrity and fluid dynamics

• The head is hydrophobic. Tail is hydrophilic

Carbohydrates

Polysaccharides + Monosaccharides

• C, H, O ; 1:2:1

Lipids

Glycerol + fatty acids

• C, H, O, and sometimes P

Lipid definition

natural molecule that doesn’t dissolve in water

• not a true polymer

Steroid

Type of lipid (fat) that works as vital structural parts of cell walls

• these chemical messengers control many body functions

Proteins

Amino Acids + Polypeptides

• C, H, O, N, S

Protein definition

large essential molecules made up of smaller building blocks (aa)

• A change in structure will change its function

Nucleic Acids

Nucleotides + RNA/DNA

• C,H,O,N,P

DNA

Deoxyribonucleic acid. This stores and transmits hereditary and genetic info.

• Small amount can be found in the mitochondria

• Usually double stranded. contains A - T, and G=-C

RNA

Ribonucleic acid. Single stranded. Helps use genetic info to make proteins and has roles in gene regulation

• Found in the nucleus, cytoplasm, and ribosomes

• Contains A, U, C, and G

Nucleotide

True monomer of nucleic acids. Made up of 5-carbon sugar, phosphate group and Nitrogenous base

• Sugar +phosphates + base

• monomer if its lacking a phosphate group

• Possible nitrogenous bases: Adenine, Guanine, Cytosine, and Thymine

Gene

Sequence of DNA that contains info used to produce a functional product

Primary structure

Exact linear sequence of amino acids linked together in a polypeptide chain

Secondary Structure

Repeating 3D shapes that forms alternating a polypeptide’s backbone or a nucleic acid chain.

• Held together by H-bonds

Tertiary Structure

3D overall shape of a single protein or polypeptide chain

Quaternary Structure

3D arrangement and assembly of 2 or more sperate polypeptide chains into a single functional protein quart structure complex

Denature

Protein or DNA loses its natural 3D shape and stops working

• Caused by Extreme heat, pH changes, or certain chemicals

Backbone of DNA?

Alternating deoxyribose sugar and phosphate groups

Relationship between protein and amino acids

If the sequence of amino acids changed in a cell the proteins unique 3D structure would change. The folding will alter and binding capabilities will be impacted

Anti-parallel

2 strands of DNA running in opposite directions

Pyrimidine

Nitrogenous base with one 6-membered ring

• DNA: C and T.

• RNA: G and A

Purine

Nitrogenous base with one 2-connected rings

• A and G